Distinguishing features of δ-proteobacterial genomes
Distinguishing features of δ-proteobacterial genomes
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DOI：
10.1073/pnas.0604311103
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发表时间：
2006-07-25
影响因子：
11.1
通讯作者：
Kaiser, Dale
中科院分区：
文献类型：
--
作者：
Karlin, Samuel;Brocchieri, Luciano;Kaiser, Dale
我们分析了五种目前可用的三角洲变形细菌基因组的几个特征，包括两种表现出掠食性行为的好氧细菌和三种厌氧硫酸盐还原细菌。这5个基因组与其他细菌有以下几个区别：(i)这5个基因组包含两个“巨型”S1核糖体蛋白基因，而其他细菌类型只有一个或没有S1；在大多数5-蛋白质细菌基因组中，主要的核糖体蛋白（RP）基因簇位于复制末端附近，而大多数细菌基因组中主要的RP基因簇位于复制起点附近；（iii） 8个基因组罕见地结合了甄别天冬酰胺和谷氨酰胺tRNA合成酶（AARS）和酰胺转移酶复合物（Gat CAB）基因，将Asp-tRNAAsn修饰为Asn-tRNA(Asn)，将gi -tRNA（Gln）修饰为Gln-tRNA(Gln)；（iv）促进吸收和去除复杂金属的TonB受体和铁载体受体在5个基因组中是共同的；(v)厌氧5基因组编码可中和过氧化氢的厌氧解毒蛋白红赤菊酯的多个拷贝；和（Vi） 0,54激活子在5个基因组中比在其他细菌中发挥更重要的作用。基因组具有过多的增强子结合蛋白，这些增强子结合蛋白对环境和细胞内信号作出反应，通常作为双组分系统的一部分；（vii） 5个基因组编码金属β -内酰胺酶的多个拷贝；（viii）一系列强调SecA、SecB和SecY的分泌蛋白可能在黄粘球菌的捕食活动中特别有用；（ix）三角洲变形杆菌在其外膜和外膜中驱动许多多蛋白机器，包括伴侣摄食机器、分泌粘液的射流和IV型菌毛。蛭弧菌在猎物细胞的周质中复制。硫酸盐还原8变形菌代谢氢并通过电子传递产生质子梯度。预测的高表达基因来自5个基因组，反映了它们不同的生态、代谢策略和适应性。
We analyzed several features of five currently available delta-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The 5 genomes are distinguished from other bacteria by several properties: (i) The 5 genomes contain two "giant" S1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no S1; (it) in most 5-proteobacterial genomes the major ribosomal protein (RP) gene cluster is near the replication terminus whereas most bacterial genomes place the major RP cluster near the origin of replication; (iii) the 8 genomes possess the rare combination of discriminating asparaginyl and glutaminyl tRNA synthetase (AARS) together with the amidotransferase complex (Gat CAB) genes that modify Asp-tRNAAsn into Asn-tRNA(Asn) and GIu-tRNA(Gln) into Gln-tRNA(Gln); (iv) the TonB receptors and ferric siderophore receptors that facilitate uptake and removal of complex metals are common among 5 genomes; (v) the anaerobic 5 genomes encode multiple copies of the anaerobic detoxification protein rubrerythrin that can neutralize hydrogen peroxide; and (Vi) 0,54 activators play a more important role in the 5 genomes than in other bacteria. 6 genomes have a plethora of enhancer binding proteins that respond to environmental and intracellular cues, often as part of two-component systems; (vii) 5 genomes encode multiple copies of metallo-beta-lactamase enzymes; (viii) a host of secretion proteins emphasizing SecA, SecB, and SecY may be especially useful in the predatory activities of Myxococcus xanthus; (ix) delta proteobacteria drive many multiprotein machines in their periplasms and outer membrane, including chaperone-feeding machines, jets for slime secretion, and type IV pili. Bdellovibrio replicates in the periplasm of prey cells. The sulfate-reducing 8 proteobacteria metabolize hydrogen and generate a proton gradient by electron transport. The predicted highly expressed genes from 5 genomes reflect their different ecologies, metabolic strategies, and adaptations.